Special Issue Information

Dear Colleagues,

Microarrays have been the first method of choice for highly parallel DNA and RNA analysis as well as in molecular interaction studies. Even though Next Generation Sequencing (NGS) is believed to soon be able to count each RNA copy in a single cell; microarrays are still irreplaceable, especially in the field of proteins, antibodies and small molecules. Nevertheless the increasing demand in throughput, molecular purity, robustness and effective production leads to improvement of the old techniques of microarray generation and to innovative ideas of ‘making’ microarrays in completely new ways. Therefore ‘the simple act’ of Microarray Generation is the focus of this Special Issue “Microarray Generation—Old Paths and New Ways”. It will highlight the old and successful paths such as light-synthesis, spot-synthesis and outline future improvements to the reader, but also offer a glimpse into what is emerging at the moment and what is yet to come, i.e., what new possibilities may become available in the not too distant future. You are invited to present new ways of microarray generation, but also to provide proof that the old ‘paths’ still bear potential for vast improvements.

With best regards,

Dr. Günter RothGuest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs).
English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Abstract: Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era.

Abstract: Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, compared to conventional protein microarrays, NAPPA technology avoids the necessity of protein purification, which is expensive and time-consuming, by substituting expression in situ with an in vitro transcription/translation kit. In summary, NAPPA arrays have been broadly employed in different studies improving knowledge about diseases and responses to treatments. Here, we review the principal advances and applications performed using this platform during the last years.

Abstract: Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano‑biological events.

Abstract: This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way to enter clinics in routine diagnostics. Protein Microarrays can be powerful tools to improve healthcare. An overview of basic characteristics to mediate essential knowledge of this technique is given. To reach this goal, some challenges still have to be addressed. A few applications of Protein Microarrays in a medical context are shown. Finally, an outlook, where the potential of Protein Microarrays is depicted and speculations how the future of Protein Microarrays will look like are made.

Abstract: Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.

Abstract: Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds remains challenging the use of antibodies may be limited in this context. In contrast to this, aptamer microarrays provide alternative techniques to circumvent these limitations. In this article we review the latest developments in aptamer microarray technology. We discuss similarities and differences between DNA and aptamer microarrays and shed light on the post synthesis immobilization of aptamers including corresponding effects on the microarray performance. Finally, we highlight current limitations and future prospects of aptamer microarray technology.

Abstract: In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.

Planned Papers

The below list represents only planned manuscripts. Some of these
manuscripts have not been received by the Editorial Office yet. Papers
submitted to MDPI journals are subject to peer-review.

Title: Label Detection and Label-free Detection for Protein MicroarraysAuthors: Amir Syahir1, Kenji Usui2,*, Kin-ya Tomizaki3, Kotaro Kajikawa4, Hisakazu Mihara5,*Affiliations:1Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang 43400, Malaysia.2Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.3Department of Materials Chemistry, Ryukoku University, Seta, Otsu 520-2194, Japan.4Department of Electronics and Applied Physics Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8502, Japan.5Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan. E-Mails: kusui@center.konan-u.ac.jpAbstract: Microarray has gone through many innovative developments in the recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early works on microarray have utilized many useful chromophores and versatile biochemical techniques dominated the high-throughput illumination. Recently the realization of label-free techniques integrating into the microarray has been greatly advanced by the combination of knowledge in material sciences, computational design, and nanofabrication. These rapidly growing new techniques are aiming at providing data without the intervention of any label molecules. Here we present a brief overview of this remarkable innovation from both perspectives of label and label-free techniques in transducing nano-biological events.

Title: Aptamer microarrays – current status and future prospectsAuthors: Martin Witt, Johanna Walter and Frank StahlAffiliation: Institut für Technische Chemie, Callinstr. 5, 30167 Hannover, GermanyAbstract: Biological research requires fast genome, proteome and transcriptome analysis technologies. Here, microarray technologies are state of the art. Since protein microarrays are limited in many experimental set-ups (e. g. multiplexing, detection of toxic targets or small molecules including organic compounds, etc.), aptamer microarrays provide alternative possibilities to circumvent these limitations.In this article we review the latest developments in aptamer microarray technology. We discuss similarities and differences between DNA-, protein and aptamer microarrays and shed light on the post synthesis immobilization of aptamers with the corresponding effects on the microarray performance. Finally we highlight current limitations and future prospects of aptamer microarray technology.

Title: Reverse Phase Protein Array - quantitative assessment of multiple biomarkers in biopsies for clinical useAuthors: Stefanie Boellner and Karl-Friedrich BeckerAffiliations: Technische Universität München, Institut für Pathologie, Trogerstrasse 18, 81675 MünchenE-Mails: kf.becker@lrz.tum.de, stefanie.boellner@tum.deAbstract: Reverse phase protein arrays (RPPA) represent a very promising high-throughput technology to monitor changes in protein levels over time, before and after treatment, between disease and non-disease states and between responders and non-responders. This array format allows quantification of one protein or phospho-protein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. After protein extraction, each patient sample is arrayed in duplicates on nitrocellulose-coated slides in a miniature dilution curve. Validated antibodies are used to detect the proteins of interest. Thus, each analyte/antibody combination can be analysed in the linear dynamic range. Current aspects of the RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.